A special thanks to Dr. Paige Scalf and her student Laura Cacciamani for compiling and creating many of the sections of this document. For more help and references to which I also am indebted see:

http://sampendu.wordpress.com/retinotopy-tutorial/ This also provides a nice psychtoolbox script that can be used to collect retinotopy data. And a script that can be used to analyze preprocessed retinotopy data. This does not however analyze the functional data in terms of preprocessing and coregistration, and we found it easier to do all the steps in FSFAST in freesurfer.

-Go to the data directories where your scanner output files are, and copy the newly created (5b) f.nii files from each of the respective EPI folders to each of the new folders in the shared folder. Make sure to put the correct files in the correct folder depending on the order of the tasks recorded in the run sheet (e.g polar positive is EPI_Vis_1 and should go in 001, polar negative is 2 and should go in 002, eccentric positive is 3, and eccentric negative is 4.

In Xubuntu > Open a terminal

8) Run recon-all on the structural data, use the -i command to import from the shared folder and create a new subject directory structure in the freesurfer subject directory (this will take all day).

recon-all -s MS_041013 -i WinShare/MS_041013.nii -all

1. Cut occiput surface
Run command

tksurfer MS_041013 lh inflated

2. to display the inflated left hemisphere.
Rotate the brain until the medial surface is facing you.
Then select points along calcarine fissure and press button “Cut line”.
Select 3 points to define the cutting plane: 2 on medial side and 1 on lateral side. Choose a 4th point to specify which portion of surface to keep and press button “Cut plane”.
Save (File > Patch > Save As) as file lh.occip.patch.3d.
(To know how to cut full brain, check out this PDF)

· in freesurfer/subjects/SUBJECTID Create a text file called “subjectname” (NO .txt on the end)

o In it should contain ONLY your subject’s name (i.e. MS_041013)

o This subject name must match the freesurfer subject name (here SUBJECTID; created when you did the recon-all command), so make sure it’s right

· Folder 001 and 002 are for Polar, 003 and 004 for eccen; In each of the 001, 002, 003, and 004 directories create a .par files (a text file with extension .par)

o They should both be called the same thing (i.e. “rtopy.par”)

o Should contain the following:

§ In folder 001:

stimtype polar

direction pos

§ In folder 002:

stimtype polar

direction neg

§ In folder 003:

stimtype eccen

direction pos

§ In folder 004:

stimtype eccen

direction neg

9)In a new window, open up the shared directory, and copy and paste the four folders into the Subject directory/Retinotopy folder with the four matching folders, the files will copy into their respective folders. Make sure the functional data matches what is written in the rtopy.par file.

10) You will also have to convert each of these f.nii files to add the TR probably:

cd 001

mri_convert f.nii f.nii -tr 2000

cd ..

cd 002

mri_convert f.nii f.nii -tr 2000

cd ..

cd 003

mri_convert f.nii f.nii -tr 2000

cd ..

cd 004

mri_convert f.nii f.nii -tr 2000

cd ..

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First-level GLM analysis:

Note: for all of these commands, you must be in the main project directory

Just a slight divergence from brain science for a second so I can put down in writing one of my genealogical histories. Priscilla Mullins was on the mayflower with her Mom Alice Atwood and dad William Mullins (who died the year the boat landed in the great sickness) She married John Alden, who also arrived […]